GapRepairer

Notice: All gaps were below 2 aa in length - they won't be described below.

Models

Number of gaps:0

Gap lengths:

Model	Entanglement	Average
		DOPE-HR
Model 1	Non-trivial	-19220
Model 2	Unknot	-18881
Model 3	Non-trivial	-19038
Model 4	Non-trivial	-18911
Model 5	Unknot	-18893
Colour the base model according to the B-factor (lowest to highest)			Reload

Warning: All models are renumbered - the first residue in the structure has index 1.

Mix & match

Provided protein had only one gap - thus there are no gap-filling combinations to be made.

EntanglementHelpKnotProtLassoProtLinkProt

Model	Type		Knot core	Slipknot	Lasso	Piercing	Show
			range	loop range	loop	position	in JSmol
Model 1	Lasso	L_+1N	--	--	41-96	+37
Model 3	Lasso	L_+1N	--	--	41-96	+37
Model 4	Lasso	L_+1N	--	--	41-96	+37
							None

Topologies marked by an OK sign () are in accordance with the template topology.

Warning: Entanglement type is assigned automatically - for more complicated topologies there may be some disagreements with manually curated databases.

Lasso thumbnails

Lasso help

Model 1

Model 3

Model 4

DOPE (Discrete Optimized Protein Energy) score per residue. The lower the score, the better.
Since DOPE is calculated against the neighbours of a given amino acid, the scores
can vary between unmoved segments of different models. See here for more information.

Warning: No templates were used. Models were generated using de novo prediction. Possible reasons include: no homologues similar enough; homologues do not cover the gaps in the target; all gaps at most 2 amino acids long.

Download Files Models Similarity profile Modelling alignment

Job Log

Wed Nov 29 09:29:13 2017	JOB CREATED : 01426d78-c9ac-45de-bce9-22a8ef8c5a10
Wed Nov 29 09:30:01 2017	STATUS CHANGED : N -> R
Wed Nov 29 09:30:01 2017	INFO : JOB STARTED AT: 2017-11-29 09:30:01.742280
Wed Nov 29 09:30:01 2017	INFO : METHOD: 1
Wed Nov 29 09:30:01 2017	INFO : Building Profile...
Wed Nov 29 09:30:01 2017	INFO : --E-value set to 0.001--
Wed Nov 29 09:38:42 2017	INFO : Homologue pool found...
Wed Nov 29 09:38:42 2017	INFO : Verifying structure sequences of homologues...
Wed Nov 29 09:53:31 2017	INFO : Starting homologue filtering...
Wed Nov 29 09:53:59 2017	INFO : Getting structures from PDB...
Wed Nov 29 09:53:59 2017	INFO : Creating modelling alignment...
Wed Nov 29 09:53:59 2017	INFO : Modelling...
Wed Nov 29 09:54:10 2017	INFO : Model 1 built
Wed Nov 29 09:54:10 2017	INFO : Validating Calpha distances...
Wed Nov 29 09:54:10 2017	INFO : Model 1 distances correct: True
Wed Nov 29 09:54:10 2017	INFO : Modelling...
Wed Nov 29 09:54:19 2017	INFO : Model 2 built
Wed Nov 29 09:54:19 2017	INFO : Validating Calpha distances...
Wed Nov 29 09:54:19 2017	INFO : Model 2 distances correct: True
Wed Nov 29 09:54:19 2017	INFO : Modelling...
Wed Nov 29 09:54:29 2017	INFO : Model 3 built
Wed Nov 29 09:54:29 2017	INFO : Validating Calpha distances...
Wed Nov 29 09:54:29 2017	INFO : Model 3 distances correct: True
Wed Nov 29 09:54:29 2017	INFO : Modelling...
Wed Nov 29 09:54:38 2017	INFO : Model 4 built
Wed Nov 29 09:54:38 2017	INFO : Validating Calpha distances...
Wed Nov 29 09:54:38 2017	INFO : Model 4 distances correct: True
Wed Nov 29 09:54:38 2017	INFO : Modelling...
Wed Nov 29 09:54:46 2017	INFO : Model 5 built
Wed Nov 29 09:54:46 2017	INFO : Validating Calpha distances...
Wed Nov 29 09:54:46 2017	INFO : Model 5 distances correct: True
Wed Nov 29 09:54:55 2017	INFO : Finished modelling
Wed Nov 29 09:54:55 2017	STATUS CHANGED : R -> P
Wed Nov 29 09:54:55 2017	INFO : Checking topology...
Wed Nov 29 09:55:09 2017	INFO : Knot matrices done...
Wed Nov 29 09:55:09 2017	INFO : No knots found...
Wed Nov 29 09:55:09 2017	INFO : Some lassos found!
Wed Nov 29 09:55:09 2017	INFO : Finishing...
Wed Nov 29 09:55:10 2017	INFO : Job done
Wed Nov 29 09:55:10 2017	STATUS CHANGED : P -> F
Wed Nov 29 09:55:10 2017	STATUS CHANGED : F -> F

1RXD chain C